How to generate a 3D binary matrix after applying a remesh modifier
Alright, if I understood your question correctly, you want a lot of ones and     zeros from a 3D mesh. Here's a script:

import bpy

object = bpy.data.objects['Suzanne']
radius = 2.0
resolution = 20
file = open("C:\\tmp\\out.txt", 'w')

import mathutils
from mathutils import Vector
def pointInsideMesh(point,ob):
 axes = [ mathutils.Vector((1,0,0)) ]
 outside = False
 for axis in axes:
    mat = ob.matrix_world
    mat.invert()
    orig = mat*point
    count = 0
    while True:
        location,normal,index = ob.ray_cast(orig,orig+axis*10000.0)
        if index == -1: break
        count += 1
        orig = location + axis*0.00001
    if count%2 == 0:
    outside = True
    break
return not outside

bla = radius/resolution

out = ""

for z in range(-resolution, resolution):
    for y in range(-resolution, resolution):
        for x in range(-resolution, resolution):
            loc = Vector((x*bla, y*bla, z*bla))
            print(loc)
            if(pointInsideMesh(loc, object) == True):
                out += '1'
            else:
                out += '0'
        out += '\n'
    out += '\n'
file.write(out)
file.close()


Again, I'm not fully sure this will answer your question, but I had fun making this script.